Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Comparative analysis of commonly used peak calling programs for ChIP-Seq analysis

  • Jeon, Hyeongrin (Department of Life Sciences, Pohang University of Science and Technology (POSTECH)) ;
  • Lee, Hyunji (Department of Life Sciences, Pohang University of Science and Technology (POSTECH)) ;
  • Kang, Byunghee (Department of Life Sciences, Pohang University of Science and Technology (POSTECH)) ;
  • Jang, Insoon (Department of Life Sciences, Pohang University of Science and Technology (POSTECH)) ;
  • Roh, Tae-Young (Department of Life Sciences, Pohang University of Science and Technology (POSTECH))
  • Received : 2020.10.06
  • Accepted : 2020.11.22
  • Published : 2020.12.31
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Abstract

Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq) is a powerful technology to profile the location of proteins of interest on a whole-genome scale. To identify the enrichment location of proteins, many programs and algorithms have been proposed. However, none of the commonly used peak calling programs could accurately explain the binding features of target proteins detected by ChIP-Seq. Here, publicly available data on 12 histone modifications, including H3K4ac/me1/me2/me3, H3K9ac/me3, H3K27ac/me3, H3K36me3, H3K56ac, and H3K79me1/me2, generated from a human embryonic stem cell line (H1), were profiled with five peak callers (CisGenome, MACS1, MACS2, PeakSeq, and SISSRs). The performance of the peak calling programs was compared in terms of reproducibility between replicates, examination of enriched regions to variable sequencing depths, the specificity-to-noise signal, and sensitivity of peak prediction. There were no major differences among peak callers when analyzing point source histone modifications. The peak calling results from histone modifications with low fidelity, such as H3K4ac, H3K56ac, and H3K79me1/me2, showed low performance in all parameters, which indicates that their peak positions might not be located accurately. Our comparative results could provide a helpful guide to choose a suitable peak calling program for specific histone modifications.

Keywords

Acknowledgement

This work was supported by grants from the National Research Foundation of Korea (NRF-2014M3C9A3064548 and NRF-2017M3C9A6047625) and BK21 Plus program funded by the Ministry of Education, Republic of Korea (10Z20130012243).

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